AMBER Archive (2006) - May 2006 By ThreadMost recent messages
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Starting: Mon May 01 2006 - 08:35:56 CDT
Ending: Wed May 31 2006 - 18:27:16 CDT
- AMBER: sequential execution of number of parallel jobs In Hee Park (Mon May 01 2006 - 15:13:23 CDT)
- AMBER: distance restraints mkseo (Mon May 01 2006 - 16:49:21 CDT)
- AMBER: some new tutorials David A. Case (Mon May 01 2006 - 18:55:19 CDT)
- AMBER: How does amber calculate HB? Li Su (Mon May 01 2006 - 20:01:05 CDT)
- AMBER: AMBER Workshops, London UK 26th - 30th June 2006 Ross Walker (Tue May 02 2006 - 10:45:33 CDT)
- AMBER: Simulation of crystal - problem with excluded atom list Jennie Thomas (Tue May 02 2006 - 12:07:20 CDT)
- AMBER: MPI parallel problem in AMBER 8.0 mkseo (Tue May 02 2006 - 16:21:50 CDT)
- AMBER: Shared libraries error Andrew Box (Tue May 02 2006 - 22:14:38 CDT)
- AMBER: proper restart procedure? John J. Love (Tue May 02 2006 - 22:33:57 CDT)
- AMBER: Question bonds and angles in frcmod and lib files Jennie Thomas (Wed May 03 2006 - 03:02:55 CDT)
- AMBER: Error while running test.serial in Amber9 Priti Hansia (Wed May 03 2006 - 06:03:27 CDT)
- AMBER: cluster architecture for the best amber performance Kateryna Miroshnychenko (Wed May 03 2006 - 07:54:58 CDT)
- AMBER: concatenating .mdcrd files Kenley Barrett (Wed May 03 2006 - 11:31:59 CDT)
- AMBER: question about group format Holly Freedman (Wed May 03 2006 - 14:18:36 CDT)
- [Fwd: Re: AMBER: Question bonds and angles in frcmod and lib files] Jennie Thomas (Wed May 03 2006 - 16:49:19 CDT)
- Re: [Fwd: Re: AMBER: Question bonds and angles in frcmod and lib files] Bill Ross (Wed May 03 2006 - 17:00:58 CDT)
- AMBER: Amber install on RedHat Linux a a (Wed May 03 2006 - 21:17:14 CDT)
- AMBER: carnal prob bala (Thu May 04 2006 - 02:44:53 CDT)
- AMBER: conflicting types for XawScrolledTableSetLocation K. Yarem (Thu May 04 2006 - 10:43:57 CDT)
- AMBER: molsurf.c error Miguel Ferreira (Thu May 04 2006 - 11:00:31 CDT)
- AMBER: amber9 serial compilation error Arvind Marathe (Thu May 04 2006 - 11:55:39 CDT)
- Re: AMBER: carnal prob Bill Ross (Thu May 04 2006 - 12:31:22 CDT)
- AMBER: lipid bi-layer system Lwin, ThuZar (Thu May 04 2006 - 12:41:11 CDT)
- AMBER: restraintmask Joseph Fernandez (Thu May 04 2006 - 13:22:21 CDT)
- AMBER: Problem with shared libraries: libimf.so Priti Hansia (Fri May 05 2006 - 12:55:39 CDT)
- AMBER: experiences with compiling amber9 for FreeBSD M. L. Dodson (Fri May 05 2006 - 13:37:19 CDT)
- AMBER: xleap on iMac G5 Evan Kelly (Fri May 05 2006 - 23:01:53 CDT)
- AMBER: AMBER9 INSTALLATION problem on O2 sgi system S.Sundar Raman (Sun May 07 2006 - 02:10:15 CDT)
- AMBER: xleap not recognizing residue Kenley Barrett (Sun May 07 2006 - 19:13:13 CDT)
- AMBER: question on distance calculation bala (Mon May 08 2006 - 05:09:23 CDT)
- AMBER: Amber9 test error on SGI Altix amit_at_mbu.iisc.ernet.in (Mon May 08 2006 - 12:14:19 CDT)
- AMBER: Problem with impose in lep Osmar Norberto de Souza (Mon May 08 2006 - 12:31:16 CDT)
- AMBER: IA64 / Altix Amber 9 Intel Compiler Problems. l_fc_c_9.0.031 Ross Walker (Mon May 08 2006 - 13:13:11 CDT)
- AMBER: Intel compiler version 9.0.033 Ross Walker (Mon May 08 2006 - 14:40:23 CDT)
- AMBER: PMEMD compilation error Joseph Fernandez (Mon May 08 2006 - 14:37:03 CDT)
- AMBER: About the Amber trajectories converted to XPLOR ( = DCD) format wang (Tue May 09 2006 - 01:25:47 CDT)
- AMBER: San Fransisco Amber users homeira amirkhani (Tue May 09 2006 - 06:38:06 CDT)
- AMBER: Amber9 test error on SGI Altix Priti Hansia (Tue May 09 2006 - 10:18:02 CDT)
- AMBER: RE: Intel Compiler. Ross Walker (Tue May 09 2006 - 11:05:28 CDT)
- AMBER: bug in ambpdb (AMBER8) Petr Kulhanek (Wed May 10 2006 - 05:54:55 CDT)
- AMBER: problem with prep file Simon Whitehead (Wed May 10 2006 - 05:52:32 CDT)
- AMBER: Hexahydrated Counterions Mahalakshmi Sahasranaman (Wed May 10 2006 - 08:22:02 CDT)
- [Fwd: AMBER: Problem with impose in lep] Osmar Norberto de Souza (Wed May 10 2006 - 12:09:48 CDT)
- Re: AMBER: xleap not recognizing residue--I fixed it, but I'm not sure why Kenley Barrett (Wed May 10 2006 - 14:54:46 CDT)
- AMBER: I'm very sorry, please disregard previous e-mail--problem seems to be fixed Kenley Barrett (Wed May 10 2006 - 15:04:16 CDT)
- AMBER: which patch for ioutfm = 1 in Amber8? Hannes Loeffler (Thu May 11 2006 - 00:21:25 CDT)
- AMBER: why the drms from sander minimization is not consistent with that from nmode ntrun=1? Pan, Yongmei (Thu May 11 2006 - 09:13:02 CDT)
- AMBER: bond information in amber snoze pa (Thu May 11 2006 - 11:48:58 CDT)
- AMBER: why the perturbation from PHE to ALA is not stable with gibbs, amber 7 Pan, Yongmei (Thu May 11 2006 - 13:50:36 CDT)
- AMBER: Amber9/mpich2 performance Joseph Fernandez (Thu May 11 2006 - 17:30:03 CDT)
- AMBER: question about REDII Raffaella D'Auria (Thu May 11 2006 - 21:04:51 CDT)
- AMBER: AMBER 8 - dihedral angles when clambda=1 Ilyas Yildirim (Thu May 11 2006 - 23:57:37 CDT)
- AMBER: Xleap compilation problem Sergio Dall'Angelo (Fri May 12 2006 - 05:19:48 CDT)
- AMBER: RMSD calculation between ligands Stefan Henrich (Fri May 12 2006 - 07:09:15 CDT)
- AMBER: another question: is rms 2E-2 good for nmode ntrun=1? Pan, Yongmei (Fri May 12 2006 - 10:22:00 CDT)
- AMBER: binpos file Varsha Goyal (Fri May 12 2006 - 15:46:24 CDT)
- AMBER: strange mm_pbsa output alfredoq_at_fcq.unc.edu.ar (Sat May 13 2006 - 10:44:58 CDT)
- AMBER: Compilers and libraries for AMBER in HPC! Pradipta Bandyopadhyay (Sun May 14 2006 - 08:25:07 CDT)
- AMBER: PBS script for lemieux Stern, Julie (Sun May 14 2006 - 18:09:30 CDT)
- AMBER: the parallel efficiency of my sander and pmemd descended rapidly with increasing CPUs Zhihong Yu (Sun May 14 2006 - 22:55:51 CDT)
- AMBER: AMBER9 compilation error on IBM Cluster amit_at_mbu.iisc.ernet.in (Mon May 15 2006 - 06:11:50 CDT)
- AMBER: Problem with "impose" in leap Osmar Norberto de Souza (Mon May 15 2006 - 06:27:13 CDT)
- AMBER: fail to execute addles pang zhao (Mon May 15 2006 - 06:59:10 CDT)
- AMBER: ff02 + POL3 problem ! Pradipta Bandyopadhyay (Mon May 15 2006 - 08:53:20 CDT)
- AMBER: installation problem Mahalakshmi Sahasranaman (Mon May 15 2006 - 13:12:51 CDT)
- AMBER: density mathew k varghese (Mon May 15 2006 - 23:02:51 CDT)
- AMBER: amber8 compiled erro on opteron with 64 bit renyanliang (Tue May 16 2006 - 04:15:24 CDT)
- AMBER: trouble stripping waters with ptraj Adam Pelzer (Tue May 16 2006 - 15:09:30 CDT)
- AMBER: amber compilation on Red Hat 8 with MPICH kawamura_hiro_at_riken.jp (Wed May 17 2006 - 00:38:35 CDT)
- AMBER: "atom number exceeds the MAXATOM" BAUVAIS_at_itodys.jussieu.fr (Wed May 17 2006 - 00:54:24 CDT)
- AMBER: distance dependent dielectric constant Mahalakshmi Sahasranaman (Wed May 17 2006 - 05:36:55 CDT)
- AMBER: "The system has extended beyond" error message Atsutoshi Okabe (Thu May 18 2006 - 00:04:31 CDT)
- AMBER: Correlation matrix used in quasih (Amber 7) Craig Gough (Thu May 18 2006 - 02:06:03 CDT)
- AMBER: AMBER9 installation error on Compaq machine. Soonmin Jang (Thu May 18 2006 - 02:11:46 CDT)
- AMBER: vlimit exceeded aixiaoli (Thu May 18 2006 - 03:14:29 CDT)
- AMBER: problem with installation, or bug? Kenley Barrett (Thu May 18 2006 - 05:09:10 CDT)
- AMBER: force field parameters Douali, Latifa (Thu May 18 2006 - 12:33:35 CDT)
- AMBER: RMSd calculations Claire Zerafa (Thu May 18 2006 - 14:25:57 CDT)
- AMBER: OT: software to support AMBER? Steve Gwaltney (Thu May 18 2006 - 13:37:06 CDT)
- AMBER: Compiling parallel Amber 9 on Red-Hat Enterprise 64 problem Hall, Spencer (Thu May 18 2006 - 17:44:14 CDT)
- AMBER: Intel fortran compiler 7? Simon Whitehead (Fri May 19 2006 - 04:47:55 CDT)
- AMBER: Fw: RMSd calculations Claire Zerafa (Fri May 19 2006 - 07:07:30 CDT)
- AMBER: problem loading forcefield leaprc.ff86 Mahalakshmi Sahasranaman (Fri May 19 2006 - 09:27:38 CDT)
- AMBER: RE: PMEMD compilation problems Simon Whitehead (Fri May 19 2006 - 10:37:46 CDT)
- AMBER: amber .off file format question Ilyas Yildirim (Fri May 19 2006 - 21:30:55 CDT)
- AMBER: RE: trouble stripping waters with ptraj Adam Pelzer (Sat May 20 2006 - 11:00:12 CDT)
- AMBER: Problem with running xleap remotely heaton_at_chem.utah.edu (Sat May 20 2006 - 14:20:27 CDT)
- AMBER: RMSd error Claire Zerafa (Mon May 22 2006 - 03:52:34 CDT)
- AMBER: Water density output Navnit Kumar Mishra (Mon May 22 2006 - 06:02:48 CDT)
- AMBER: A dummy atom on the center of solute molecule Atsutoshi Okabe (Mon May 22 2006 - 06:49:23 CDT)
- AMBER: Macromodel Amber* vs. Amber7 opitz_at_che.udel.edu (Mon May 22 2006 - 07:56:54 CDT)
- AMBER: More Amber 9 Benchmarks available Robert Duke (Mon May 22 2006 - 09:23:15 CDT)
- AMBER: Again SASA lucas luquitas (Mon May 22 2006 - 14:51:22 CDT)
- AMBER: 3Dsig: Struct Bioinfo & Comp Biophysics Meeting, 4-5 Aug. Brazil 3Dsig06 (Mon May 22 2006 - 17:03:45 CDT)
- AMBER: error in AMBER 9.0 mkseo (Tue May 23 2006 - 16:43:28 CDT)
- AMBER: amber8 bugfix effects kawamura_hiro_at_riken.jp (Wed May 24 2006 - 03:17:32 CDT)
- AMBER: simulate proteins with non-standard residues Hui Lei (Wed May 24 2006 - 12:10:08 CDT)
- AMBER: freeze interval vibrations Eric Hu (Wed May 24 2006 - 12:52:47 CDT)
- AMBER: problem with prepfile Shafinaz (Wed May 24 2006 - 14:50:21 CDT)
- AMBER: use_pme=0 problem luckyang_at_gmail.com (Wed May 24 2006 - 18:18:47 CDT)
- AMBER: output of first stage RESP calculation JunJun Liu (Wed May 24 2006 - 17:23:55 CDT)
- AMBER: How to built the deprotonated form of lysine and tyrosine jitrayut jitonnom (Wed May 24 2006 - 21:49:04 CDT)
- AMBER: Fwd: RESP for deprotonated tyrosine and lysine jitrayut jitonnom (Wed May 24 2006 - 21:57:45 CDT)
- AMBER: Qestion about input for RESP program JunJun Liu (Wed May 24 2006 - 21:44:41 CDT)
- AMBER: How to build NH2 of amino acid in amber jitrayut jitonnom (Wed May 24 2006 - 22:52:25 CDT)
- AMBER: question about QM/MM in amber9 aixiaoli (Thu May 25 2006 - 03:37:10 CDT)
- AMBER: New united atom force field and GB solvation model in amber9 (leaprc.ff03ua) Soonmin Jang (Thu May 25 2006 - 05:51:02 CDT)
- AMBER: 1st 2 lines of restart files hayden (Thu May 25 2006 - 06:40:03 CDT)
- AMBER: alpha helix preference problem harianto (Thu May 25 2006 - 16:16:23 CDT)
- AMBER: RMSd error Claire Zerafa (Thu May 25 2006 - 23:37:54 CDT)
- AMBER: RE: trouble stripping waters with ptraj Adam Pelzer (Thu May 25 2006 - 23:50:53 CDT)
- AMBER: ptraj: calculating distances between atoms in charges residues Magne Olufsen (Fri May 26 2006 - 02:13:48 CDT)
- AMBER: Question about .off file Sergey Krishtal (Fri May 26 2006 - 03:15:06 CDT)
- AMBER: different TI calculations starting from the same state Andrea Bortolato (Fri May 26 2006 - 08:56:47 CDT)
- AMBER: different TI calculations starting from the same state Andrea Bortolato (Fri May 26 2006 - 05:12:12 CDT)
- AMBER: Saving RMSD values in VMD nag raj (Fri May 26 2006 - 09:33:00 CDT)
- AMBER: check as error: load prepin in tleap jitrayut jitonnom (Fri May 26 2006 - 12:13:41 CDT)
- AMBER: Please reply Shafinaz (Fri May 26 2006 - 14:19:42 CDT)
- AMBER: Installing / Compiling Question Seth Lilavivat (Fri May 26 2006 - 22:29:06 CDT)
- AMBER: md error : sander jitrayut jitonnom (Sun May 28 2006 - 13:11:45 CDT)
- AMBER: which time should I use to calculate the number of "ps/Day" Zhihong Yu (Mon May 29 2006 - 04:32:26 CDT)
- AMBER: antechamber help needed for FAD pkb bioinfo (Mon May 29 2006 - 04:38:48 CDT)
- AMBER: Difference in results for TI calculation brmeher_at_iitg.ernet.in (Mon May 29 2006 - 08:53:41 CDT)
- AMBER: Difference in results for TI calculation brmeher_at_iitg.ernet.in (Mon May 29 2006 - 09:23:45 CDT)
- AMBER: problems with antechamber JAVIER PEREZ (Mon May 29 2006 - 10:04:52 CDT)
- AMBER: energy terms JAVIER PEREZ (Mon May 29 2006 - 10:25:31 CDT)
- AMBER: SAVEPDB in Xleap could not save 4 character atom names Jiayun Pang (Mon May 29 2006 - 11:38:22 CDT)
- Re: AMBER: SAVEPDB in Xleap could not save 4 character atom names Bill Ross (Mon May 29 2006 - 15:26:56 CDT)
- AMBER: Different results for TI calculation Biswa Ranjan Meher (Wed May 31 2006 - 02:25:13 CDT)
- AMBER: Replica exchage: about exchange interval Atsutoshi Okabe (Wed May 31 2006 - 07:36:27 CDT)
- AMBER: Force units in forcedump.dat Steven Winfield (Wed May 31 2006 - 08:41:43 CDT)
- AMBER: Namelists in input files Steven Winfield (Wed May 31 2006 - 11:42:05 CDT)
- AMBER: SHAKE, TIP3P and 2fs Timesteps Mark Williamson (Wed May 31 2006 - 12:32:56 CDT)
- AMBER: xleap problem and answer Thomas Pochapsky (Wed May 31 2006 - 13:32:32 CDT)
- AMBER: AMBER mdcrd file bigger than 2GB snoze pa (Wed May 31 2006 - 16:57:22 CDT)
- AMBER: Installation of Amber8 on Fedora Core 5 DAVID P. RANGEL (Wed May 31 2006 - 17:48:11 CDT)
Last message date: Sat Dec 30 2006 - 07:20:23 CST
Archived on: Wed Feb 21 2007 - 22:44:16 CST
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